add bwameth/index module + test

.github/filters.yml

@@ -96,6 +96,10 @@ bwamem2_mem:
   - software/bwamem2/mem/**
   - tests/software/bwamem2/mem/**
 
+bwameth_index:
+  - software/bwameth/index/**
+  - tests/software/bwameth/index/**
+
 cat_fastq:
   - software/cat/fastq/**
   - tests/software/cat/fastq/**

software/bwameth/index/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bwameth/index/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BWAMETH_INDEX {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
+    } else {
+        container "quay.io/biocontainers/bwameth:0.20--py35_0"
+    }
+
+    input:
+    path fasta
+
+    output:
+    path "*.bwameth.c2t*", emit: index
+    path "*.version.txt" , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    bwameth.py index $fasta
+
+    echo \$(bwameth.py --version 2>&1) | cut -f2 -d" " > ${software}.version.txt
+    """
+}

software/bwameth/index/meta.yml

@@ -0,0 +1,53 @@
+name: bwameth_index
+description: Performs indexing of c2t converted reference genome
+keywords:
+    - bwameth
+    - 3-letter genome
+    - index
+    - methylseq
+    - bisulphite
+    - fasta
+tools:
+    - bwameth:
+        description: |
+            Fast and accurate alignment of BS-Seq reads
+            using bwa-mem and a 3-letter genome.
+        homepage: https://github.com/brentp/bwa-meth
+        documentation: https://github.com/brentp/bwa-meth
+        arxiv: arXiv:1401.1129
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - fasta:
+        type: file
+        description: Input genome fasta file
+output:
+    - index:
+        type: file
+        description: c2t converted genome BWA index files
+        pattern: "*.{bwameth.c2t.amb,bwameth.c2t.ann,bwameth.c2t.bwt,bwameth.c2t.pac,bwameth.c2t.sa}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

tests/software/bwameth/index/main.nf

@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] )
+
+workflow test_bwameth_index {
+
+    BWAMETH_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
+}

tests/software/bwameth/index/test.yml

@@ -0,0 +1,18 @@
+- name: Run bwameth index test workflow
+  command: nextflow run ./tests/software/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
+  tags:
+    - bwameth
+    - bwameth_index
+  files:
+    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.pac
+      md5sum: 7586c6a3be45c4dea15376a5c7bb9bf0
+    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.amb
+      md5sum: 87e019665cbb66bdee2bacccb26845c9
+    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.ann
+      md5sum: a4659a63572b6998c67457bd8e95790d
+    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.bwt
+      md5sum: 582854008bcbe99d5b51290773a7db5f
+    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t
+      md5sum: db670853725f4a31080c991e9df6b330
+    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.sa
+      md5sum: 020db07e7e1544dc961c30c9936f3213